Re: [gmx-users] trjconv -pbc nojump across multiple trajectories

[Tsjerk Wassenaar]

Hi Pablo,

You can use trjcat to stitch the parts of your trajectory together.
A .cpt file contains information about the state, the positions and such.
It doesn't contain static information, like residue/atom names, which are
needed for a reference structure.

Cheers,

Tsjerk


On Thu, Nov 22, 2012 at 3:34 PM, Pablo Englebienne  wrote:

> Hi all,
>
> I am planning to run a 100ns simulation by continuing a simulation in
> increments of 1ns. After each round, analyses are performed and the
> trajectory scrapped. One of the analysis I need to do is mean square
> displacement; for this I need a continuous trajectory as provided by
> trjconv -pbc nojump.
>
> The issue that I have is how to make sure that the trajectory stays
> continuous across the different time increments. By reading the manual of
> trjconv, I found out that "the starting configuration for this procedure is
> taken from the structure file, if one is supplied, otherwise it is the
> first frame." I thought of using the .cpt file from the previous step as
> structure file (trjconv -s) for trjconv, but .cpt is not one of the formats
> accepted for that option (only tpr, tpb, tpa, gro, g96, pdb).
>
> The other issue is that as the dumping of snapshots is performed
> frequently (every 100 timesteps) I would be using double precision, so I
> would like to use a double-precision structure to do the "nojump" step as
> well. A cpt file seems to be perfectly suited for this, as well as a
> single-frame trr file, however neither of them is accepted as a structure
> file for trjconv.
>
> My questions are 2:
>  1. what would be the best way to ensure a continuous trajectory across
> multiple fragments of a trajectory, using double precision?
>  2. is there a specific reason why a cpt is not accepted as a structure
> file for trjconv -s?
>
> Thanks for your comments!
>
> Regards,
> Pablo
>
> --
>
> Dr. Pablo Englebienne
> Postdoctoral Researcher
>
> *TU Delft / 3mE / Process & Energy*
> /Engineering Thermodynamics (ETh) group/
>
> Building 46
> Leeghwaterstraat 44, room 030
> 2628 CA Delft
> The Netherlands
>
> *T* +31 (0)15 27 86662 
> *E* p.englebie...@tudelft.nl 
>  >
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
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[gmx-users] trjconv -pbc nojump across multiple trajectories

[Pablo Englebienne]

Hi all,

I am planning to run a 100ns simulation by continuing a simulation in 
increments of 1ns. After each round, analyses are performed and the 
trajectory scrapped. One of the analysis I need to do is mean square 
displacement; for this I need a continuous trajectory as provided by 
trjconv -pbc nojump.


The issue that I have is how to make sure that the trajectory stays 
continuous across the different time increments. By reading the manual 
of trjconv, I found out that "the starting configuration for this 
procedure is taken from the structure file, if one is supplied, 
otherwise it is the first frame." I thought of using the .cpt file from 
the previous step as structure file (trjconv -s) for trjconv, but .cpt 
is not one of the formats accepted for that option (only tpr, tpb, tpa, 
gro, g96, pdb).


The other issue is that as the dumping of snapshots is performed 
frequently (every 100 timesteps) I would be using double precision, so I 
would like to use a double-precision structure to do the "nojump" step 
as well. A cpt file seems to be perfectly suited for this, as well as a 
single-frame trr file, however neither of them is accepted as a 
structure file for trjconv.


My questions are 2:
 1. what would be the best way to ensure a continuous trajectory across 
multiple fragments of a trajectory, using double precision?
 2. is there a specific reason why a cpt is not accepted as a structure 
file for trjconv -s?


Thanks for your comments!

Regards,
Pablo

--

Dr. Pablo Englebienne
Postdoctoral Researcher

*TU Delft / 3mE / Process & Energy*
/Engineering Thermodynamics (ETh) group/

Building 46
Leeghwaterstraat 44, room 030
2628 CA Delft
The Netherlands

*T* +31 (0)15 27 86662 
*E* p.englebie...@tudelft.nl 

--
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